Variant report

Variant	rs2424553
Chromosome Location	chr20:23403939-23403940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23337918..23344174-chr20:23400107..23404916,9	MCF-7	breast:
2	chr1:144534221..144535752-chr20:23402845..23404345,2	K562	blood:
3	chr20:23345633..23349899-chr20:23400854..23404181,4	K562	blood:
4	chr20:23340954..23342681-chr20:23403293..23405458,3	MCF-7	breast:
5	chr20:23345633..23349899-chr20:23400647..23404181,5	K562	blood:

Variant related genes	Relation type
ENSG00000232645	Chromatin interaction
ENSG00000125812	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1003417	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1419008	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs2144381	1.00[YRI][hapmap]
rs2251145	0.83[AFR][1000 genomes]
rs2281430	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2405231	0.88[EUR][1000 genomes]
rs2424529	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs2424533	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2424534	0.93[ASW][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2424535	0.81[AFR][1000 genomes]
rs2424537	0.81[AFR][1000 genomes]
rs2424538	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2424541	0.81[AFR][1000 genomes]
rs2424543	1.00[CEU][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2424544	0.83[AFR][1000 genomes]
rs2424545	0.93[ASW][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2424547	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2424549	0.83[AFR][1000 genomes]
rs2424550	0.83[AFR][1000 genomes]
rs2424551	0.83[AFR][1000 genomes]
rs4813495	0.83[AFR][1000 genomes]
rs4815199	1.00[YRI][hapmap]
rs6048777	0.88[EUR][1000 genomes]
rs6048778	0.86[ASW][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs6048797	0.87[EUR][1000 genomes]
rs6076065	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6083099	1.00[YRI][hapmap]
rs6083100	1.00[YRI][hapmap]
rs6083104	0.93[ASW][hapmap];1.00[YRI][hapmap]
rs6083105	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6083106	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6083111	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6132607	0.93[ASW][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6137934	0.83[AFR][1000 genomes]
rs6137940	0.83[AFR][1000 genomes]
rs743021	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs743024	0.93[ASW][hapmap];1.00[YRI][hapmap]
rs761723	0.81[CEU][hapmap]
rs761726	0.85[AFR][1000 genomes]
rs7988	0.86[ASW][hapmap]
rs999072	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063655	chr20:23396649-23489730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2424553	NAPB	cis	multi-tissue	Pritchard
rs2424553	CST9L	cis	parietal	SCAN
rs2424553	NAPB	cis	Artery Tibial	GTEx
rs2424553	GGTLC1	cis	cerebellum	SCAN
rs2424553	NAPB	cis	Esophagus Muscularis	GTEx
rs2424553	ZNF607	trans	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23402400-23406000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:23402600-23404800	Weak transcription	K562	blood
3	chr20:23402600-23405600	Enhancers	Primary T cells from cord blood	blood
4	chr20:23402600-23405600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr20:23402600-23405800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr20:23402600-23405800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr20:23402600-23406000	Weak transcription	NHEK	skin
8	chr20:23402800-23404000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr20:23402800-23404200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr20:23402800-23405600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr20:23403000-23404600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr20:23403200-23406200	Enhancers	Fetal Thymus	thymus
13	chr20:23403800-23404000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr20:23403800-23405200	Weak transcription	HepG2	liver

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